Sodium in PDB 4wxb: Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus

All present enzymatic activity of Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus:
2.1.2.1;

The structure of Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus, PDB code: 4wxb was solved by K.Hernandez, I.Zelen, G.Petrillo, I.Uson, C.Wandtke, J.Bujons, J.Joglar, T.Parella, P.Clapes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.54 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.104, 113.431, 133.388, 90.00, 93.85, 90.00
R / Rfree (%)	19.1 / 22.1

The structure of Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus also contains other interesting chemical elements:

Arsenic

(As)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus (pdb code 4wxb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus, PDB code: 4wxb:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:41.1 occ:1.00 O B:PHE301 2.2 36.0 1.0 O B:PHE295 2.3 36.0 1.0 O B:HIS298 2.3 45.5 1.0 O B:ASN296 2.4 36.3 1.0 C B:ASN296 3.1 35.5 1.0 CA B:ASN296 3.4 38.5 1.0 C B:HIS298 3.4 43.1 1.0 C B:PHE295 3.5 38.9 1.0 C B:PHE301 3.5 44.7 1.0 N B:HIS298 3.7 45.4 1.0 N B:ASN296 3.9 39.5 1.0 O B:HOH661 4.0 35.4 1.0 CA B:HIS298 4.1 45.7 1.0 N B:GLN297 4.1 35.7 1.0 C B:GLN297 4.1 41.6 1.0 N B:PHE301 4.3 52.4 1.0 CA B:PHE301 4.4 46.6 1.0 N B:ARG302 4.4 41.2 1.0 CA B:ARG302 4.5 41.5 1.0 N B:PRO299 4.5 49.3 1.0 CB B:HIS298 4.6 46.9 1.0 CA B:GLN297 4.6 41.7 1.0 O B:GLN297 4.6 44.5 1.0 CB B:PHE301 4.7 43.9 1.0 CA B:PRO299 4.7 50.2 1.0 C B:PRO299 4.7 46.4 1.0 CA B:PHE295 4.8 34.5 1.0 CB B:ASN296 4.8 33.6 1.0 N B:ASP300 4.9 47.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:40.4 occ:1.00 O C:PHE301 2.3 39.0 1.0 O C:HIS298 2.4 42.8 1.0 O C:ASN296 2.5 33.5 1.0 O C:PHE295 2.6 31.8 1.0 C C:ASN296 3.2 32.9 1.0 C C:PHE301 3.5 40.6 1.0 CA C:ASN296 3.5 36.9 1.0 C C:HIS298 3.6 39.8 1.0 C C:PHE295 3.6 34.1 1.0 N C:ASN296 4.1 36.8 1.0 C C:GLN297 4.2 42.3 1.0 N C:GLN297 4.3 36.4 1.0 N C:HIS298 4.3 44.5 1.0 O C:GLN297 4.3 40.9 1.0 N C:PHE301 4.3 41.6 1.0 CA C:ARG302 4.4 36.5 1.0 N C:ARG302 4.4 35.2 1.0 CA C:PHE301 4.4 39.6 1.0 CA C:HIS298 4.5 41.0 1.0 N C:PRO299 4.5 42.5 1.0 CA C:PRO299 4.5 38.7 1.0 C C:PRO299 4.7 37.8 1.0 CB C:PHE301 4.8 36.1 1.0 CA C:GLN297 4.8 42.5 1.0 CB C:ASN296 4.9 35.4 1.0 CB C:HIS298 4.9 45.0 1.0 O C:PRO299 5.0 37.5 1.0 CA C:PHE295 5.0 32.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Serine Hydroxymethyltransferase From Streptococcus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:48.7 occ:1.00 O D:PHE301 2.3 54.2 1.0 O D:HIS298 2.4 52.0 1.0 O D:ASN296 2.4 45.2 1.0 O D:PHE295 2.5 41.6 1.0 C D:ASN296 3.1 48.1 1.0 CA D:ASN296 3.5 46.7 1.0 C D:HIS298 3.5 51.3 1.0 C D:PHE301 3.5 55.3 1.0 C D:PHE295 3.6 42.9 1.0 N D:HIS298 4.0 51.1 1.0 N D:ASN296 4.1 41.6 1.0 N D:GLN297 4.1 44.5 1.0 C D:GLN297 4.1 54.9 1.0 CA D:HIS298 4.3 48.3 1.0 CA D:ARG302 4.4 47.4 1.0 N D:ARG302 4.4 49.7 1.0 N D:PHE301 4.5 60.3 1.0 O D:GLN297 4.5 52.8 1.0 CA D:PHE301 4.5 55.3 1.0 CA D:GLN297 4.6 49.3 1.0 N D:PRO299 4.6 56.6 1.0 CA D:PRO299 4.6 49.3 1.0 CB D:PHE301 4.8 51.0 1.0 C D:PRO299 4.8 53.5 1.0 CB D:ASN296 4.9 45.5 1.0 OD1 D:ASN296 4.9 38.6 1.0 CA D:PHE295 4.9 41.0 1.0 CB D:HIS298 4.9 50.0 1.0

K.Hernandez, I.Zelen, G.Petrillo, I.Uson, C.M.Wandtke, J.Bujons, J.Joglar, T.Parella, P.Clapes. Engineered L-Serine Hydroxymethyltransferase From Streptococcus Thermophilus For the Synthesis of Alpha , Alpha-Dialkyl-Alpha-Amino Acids. Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25611820
DOI: 10.1002/ANIE.201411484